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In the classic ruleset, the first land unit that can attack from non-native-tiles is the Marine. So, defenders have ample time to research and build Coastal Defense and Musketeer in their coastal cities before they have to deal with sea-borne attacks.

In civ2civ3, the Musketeer can attack from non-native-tiles. To adequately defend against a gang of 3 pirate Musketeers, the defender needs to have Coastal Defense and Pikemen in coastal towns. This is not feasible given the research costs of Feudalism and Navigation vs just Gunpowder. The AI that runs the Pirates doesn't seem to know about this, so local games currently work fine. But other humans can pull this against you, and the AI will get fixed.

An easy way to fix this, would be to postpone non-native-tile attacks to Riflemen.

Civ2civ3 fixed several historical-order inaccuracies (Darwin/Eiffel, Iron before Destroyers, etc.). Some remaining ones are:
* What do Frigates attack non-native-tiles with, if not cannons (which need gunpowder)?
* The icon for Coastal Defense shows cannons

Maybe these could be made more sensible while fixing the non-native-tile problem with some creative thought.

Bonus defence against Musketeers is City Walls. Even if they are from the sea, they are still land units. Coastal Defense works against naval units.

About use weapon, whereas we don't have tech: make canon like turret in some ruleset and cargo of ship. Additionally made possible to trade units.

Another possibility could be:
1. Allow to require some resources to produce units
2. Add store to city - when city produces (for example) canon, it need saletra
3. Resources could been carried by caravans.

Second options adds many micromanagement.
Edit:
About second option: I forget to made two tech instead of one:
1. Metallurgy - allowing to constructing canons (gunpowder needed)
2. Gunpowder - allowing producing gunpowder (saletra needed)
3. Moving gunpowder/saletra with caravans or trade by trade